filesystem Update Error /bin exists in filesystem

Trilby · 2013-06-14 11:32:33

zero, the first of those commands does not match the one on the front page news, check again.

As far as what errors .... There were 68 scrolling lines all starting with "errore". I'm no linguist, but I'm pretty sure those are errors! I don't know how you can claim that command reported no errors.

Last edited by Trilby (2013-06-14 11:33:08)

Mr Green · 2013-06-14 12:20:00

This might be a really really bad idea but what if pacman had a pre-install warming system so any major package updates [that may cause any issue!] users are pointed to main page/news item prior to update?

Know that these system changes do not happen very often but it would certainly save having a 23 page thread.

zero-giulio · 2013-06-14 12:26:26

English translations are:

error: no package contains /bin
error: no package contains /bin/systemd
error: no package contains /sbin
(etc...)

I assume this output is telling me there is no package to be fixed (I mean, I'm querying to list a set of files (not owned by any package) but there are no such files and so I receive an error for each subdirectory for empty set.

Otherwise, how to interpret such output?
The lines are /bin, /bin/systemd, /sbin, /sbin/NetworkManager, etc...
What should I do? systemd and NetworkManager were updated during pacman -S --ignore bash,filesystem.
Should I delete such files?

As for the first command, the first time I ran it I copied/pasted the command from the homepage.
Maybe after the errore on upgrade filesystem I tried another time to run the 5 commands and this second time I wrote the query on my own instead of copy it (and I miss the other two directory) <- then I pasted this last one into forum

Trilby · 2013-06-14 12:35:31

zero, I'm not sure what you best next step(s) would be as I really have no idea what you've already done, but as a constructive criticism only meant to help you get the assistence you'll need, you need to be more precise in your posts.

Sure you know that the command you ran is not the same as the command you said you ran - but we can't know that. And if you see a string of 68 "error: ..." lines, but you report seeing no errors ... welll, that is clearly a misrepresentation of the facts. Don't blend your interpretation in with the facts. Saying "There were 68 errors, but they were not associated with any package, so I don't think they are relevant" is very different from saying "there were no errors". In the former case, you could be corrected and helped to fix those errors, in the latter case you'd have mislead your would be helpers.

On the point of solving the problem, those errors are very important. Somehow your entire pacman database is screwed. Those files *do* belong to packages - somehow you've got the files, but no entries in the database. I can only assume you did some sort of manual attempt of moving files or editting pacman's database before using the commands on the front page news. But this is only an assumption as you have not been clear in your description of what you have actually done.

Last edited by Trilby (2013-06-14 12:40:07)

jakobcreutzfeldt · 2013-06-14 12:38:43

Mr Green wrote:

This might be a really really bad idea but what if pacman had a pre-install warming system so any major package updates [that may cause any issue!] users are pointed to main page/news item prior to update?
Know that these system changes do not happen very often but it would certainly save having a 23 page thread.

Both pacnanny and pacmatic do that (see my sig; warning: some self-promotion)

zero-giulio · 2013-06-14 13:19:23

Is there a fast way to reinstall Arch (in order to avoid update problems)?

I have /home on a different partition, so I shouldn't lose program settings.
I have /var on a different partition too, so it should be sufficient to install all packages in /var/cache/pacman/pkg (I did not clean such dir) in order to come up with a complete (i.e., with all software I want) installation.

My idea is something like that:
do not touch /dev/sda5 (the /boot partition)
do not touch /dev/sda8 (the /var partition)
do not touch /dev/sda9 (the /home partition)
rewrite all files/folders on /dev/sda7 (the root partition).

Is there a fast way to do that?

(some configuration files (pacman, yaourt, lightdm, wvdial etc...) are in /etc directory, I can eventually backup them prior to format root partition).

Last edited by zero-giulio (2013-06-14 13:38:00)

Lockheed · 2013-06-14 15:09:41

I don't get that thread.

Apart from the fact that after reading it I still don't know what is the solution of the problem described in the first post,
I don't even use [testing] repository, so I shouldn't even have that issue...

I found this instruction: https://www.archlinux.org/news/binaries … ervention/
but when I get to this step:

$ paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

and I run it against all repositories I use, ie: core, extra, community, multilib, archlinuxfr
the result is absolutely nothing, which seems strange, as I have loads of packages installed from AUR through yaourt.

Last edited by Lockheed (2013-06-14 15:30:49)

ball · 2013-06-14 15:28:30

@Lockheed: Just follow the instructions in the latest news item on the home page: https://www.archlinux.org/news/binaries … ervention/
In case of errors: report back.
(Is this really that hard?)

Last edited by ball (2013-06-14 15:29:10)

Lockheed · 2013-06-14 15:31:26

ball wrote:

@Lockheed: Just follow the instructions in the latest news item on the home page: https://www.archlinux.org/news/binaries … ervention/
In case of errors: report back.
(Is this really that hard?)

I updated my post with regards to that news.

ball · 2013-06-14 15:44:18

Lockheed wrote:

but when I get to this step:
$ paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
and I run it against all repositories I use, ie: core, extra, community, multilib, archlinuxfr
the result is absolutely nothing, which seems strange, as I have loads of packages installed from AUR through yaourt.

You only have to execute this command for unofficial repos, in this case archlinuxfr. So did you execute

$ paclist archlinuxfr | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

?

If there is no output, then move on to the next step in the news.

Last edited by ball (2013-06-14 15:45:21)

Lockheed · 2013-06-14 15:45:38

Yes. It shows nothing, just like all the rest.

$ paclist archlinuxfr | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
$

But I'm pretty sure there is a lot of AUR programs that are in /usr/sbin
Will they not be lost if I continue?

Last edited by Lockheed (2013-06-14 15:50:21)

SolarBoyMatt · 2013-06-14 15:52:16

If that command shows nothing, then it's safe...

Lockheed · 2013-06-14 15:57:36

Ok, thanks. Two more questions:

1) Fix any non-official packages with files in /bin, /sbin or /usr/sbin to put those files in /usr/bin. The list of packages that are not in a repo that need to be fixed can be generated using:
$ pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -

What does it mean 'fix'?

The list of those packages is this:

$ pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
gen-init-cpio 2.6.36-1
sysvinit 2.88-9
arno-iptables-firewall 2.0.1-1
fixparts-git 20130208-1
gptfdisk-git 20130208-1
hdck 0.5.0-1
hdsentinel 0.8-1
hibernate-script 2.0-8
hostsblock 0.11.2-1
msr-tools 1.2-2
powerdown 20121019-1
proftpd 1:1.3.4c-3
schednice 20120301-1
tcp_wrappers 7.6-15
uswsusp-git 20130112-1

3) If you have files in /bin, /sbin or /usr/sbin that are unowned by any package, you need to move them

Move where? To /usr/bin?

SolarBoyMatt · 2013-06-14 16:07:46

1. If you're not using those, remove them with pacman, and then you could reinstall them after the update if you still want them. Otherwise it means they need to be rebuilt so that they install to /usr/bin instead of wherever they were.

3. Ideally there shouldn't be any like that, but if they are, they need to be moved somewhere else.

This has been answered multiple times in this thread already.

Last edited by SolarBoyMatt (2013-06-14 16:09:25)

hokasch · 2013-06-14 16:08:54

Lockheed wrote:

Apart from the fact that after reading it I still don't know what is the solution of the problem described in the first post,
I don't even use [testing] repository, so I shouldn't even have that issue...

The post was made when the changes where still in testing, they have since migrated to core. The solution is detailed in the front page instructions.

Lockheed wrote:

I found this instruction: https://www.archlinux.org/news/binaries … ervention/
but when I get to this step:
$ paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
and I run it against all repositories I use, ie: core, extra, community, multilib, archlinuxfr
the result is absolutely nothing, which seems strange, as I have loads of packages installed from AUR through yaourt.

AUR is not a (binary) repository managed by pacman. See the command before that to find local packages that need fixing. Once you pass all these (i.e. you have no files in /bin, /sbin or /usr/sbin which do not belong to an official package), procced to the three-step update described at the end.

EDIT:

you posted a list from running "pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -" - these are the aur packages you have to update / remove.

Last edited by hokasch (2013-06-14 16:17:09)

ball · 2013-06-14 16:11:36

For example sysvinit has been dropped from the official repos quite some time ago. Complete the switch to systemd before proceeding. But this has been anounced on the news page, too. Conclusion: read the Arch Linux news from time to time, even better: subscribe to the announcement list.

Last edited by ball (2013-06-14 16:15:25)

Lockheed · 2013-06-14 16:27:03

That might be a good idea. Thanks guys.

Trilby · 2013-06-14 18:40:58

@zero (RE: reinstall), you can definitely leave your home partition untouched - and should in fact keep it not mounted. The boot partition you could also leave alone, though you'll likely need to touch up your bootload config after the reinstall.

The var partition, however, will definitely need to be mounted for pacman to run. In fact, the var partition is exactly where you current problem exists: that's where pacman's database is, and where the package cache is held. Reinstalling without access to the var partition could actually get you in the exact perdicament you now find yourself in: none of the installed files would be tracked by pacman.

Last edited by Trilby (2013-06-14 18:43:44)

rcincx · 2013-06-15 05:56:25

hey guys - just here to say thanks for the awesome work and information around here, making this big upgrade quite straight-forward for me.

Mr Green · 2013-06-15 09:11:53

jakobcreutzfeldt wrote:

Mr Green wrote:
This might be a really really bad idea but what if pacman had a pre-install warming system so any major package updates [that may cause any issue!] users are pointed to main page/news item prior to update?
Know that these system changes do not happen very often but it would certainly save having a 23 page thread.
Both pacnanny and pacmatic do that (see my sig; warning: some self-promotion)

Just came across pacmatic trying it out now. Not heard of pacnanny

imiric · 2013-06-15 12:02:09

For me this was shell related. Here's how I fixed it:

1. Login as root.
2. Run `chsh <user>`
3. Pick a known shell path.

If you try to run `chsh` while logged in as your user (via `su - <user>` is the only way), you'll get the message:

your shell is not in /etc/shells, shell change denied: Permission denied

HTH.

TheSaint · 2013-06-15 13:05:35

filesystem upgrade gathered more victims
I suppose that your path is corrupted and then it cannot find the executables.
Try to reinstall from outside the partition like Pacman -S base -r /dev/disk/where/you/have/arch

Last edited by TheSaint (2013-06-15 13:06:01)

HeartsAlive · 2013-06-15 14:36:01

I still haven't solved this... tried reinstalling from outside the partition but I still get the failed to initialize alpm library problem. Do I need to mount something before pacman will work correctly from outside the partition?

Don Coyote · 2013-06-15 15:07:51

I'm not sure if my sense of written language is in conflict with any others', but if the announcement:

5) Update your system.
Before performing this update, you may want to ensure you have a second terminal open with root privileges in the unlikely event of an emergency, particularly if updating over ssh.
# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su

Had instead read:

5) Update your system.
(Before performing this update, you may want to ensure you have a second terminal open with root privileges in the unlikely event of an emergency, particularly if updating over ssh.)
# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su

or

5) Before performing this update, you may want to ensure you have a second terminal open with root privileges in the unlikely event of an emergency, particularly if updating over ssh.
Update your system.
# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su

It would have saved me a few hours of poking around the forums. The current formatting implies to me that the code block is a continuation of the supplementary instructions and the core instructions are simply to 'update your system', which continues to give the error. Yes, reading the 'suggestion' and contents of the block makes it clear the two are not conncected, but disregarding unneeded text is second nature when perusing the web, particularly branching instructions associated with an open system like this.

zero-giulio · 2013-06-15 15:16:09

I restore a clonezilla backup.
I did not touch /boot, /home and /var partiotins, while root partition was restored from the clonezilla backup (dated 2013-02-02).

Actually I have at least a working system.

My idea was to perform two distinct update:
1) update as at 2013-05-27 first;
2) update at current date then.

The idea is first to update at a recent state but before the move of the bin' folders, and finally re-try to update.
(I choose 2013-05-27 because my previous successful upgrade was done in such date and so I have all the required package in cache <- no downloads required, very important for me as I have a slow connection)

First, I set arm.konnichi etc in mirrorlist and then I ran pacman -Syy.
Ok.

Then I try to do a pacman -S pacman.
Maybe this was not a good idea as now I can use no longer pacman:

pacman: error while loading shared libraries: libarchive.so.13: cannot open shared object file: No such file or directory

Upgrade from clonezilla backup (dated Febrary 2013) is not so simple maybe.

How to solve problem with libarchive?

Last edited by zero-giulio (2013-06-15 15:29:54)

Arch Linux

#576 2013-06-14 11:32:33

Re: filesystem Update Error /bin exists in filesystem

#577 2013-06-14 12:20:00

Re: filesystem Update Error /bin exists in filesystem

#578 2013-06-14 12:26:26

Re: filesystem Update Error /bin exists in filesystem

#579 2013-06-14 12:35:31

Re: filesystem Update Error /bin exists in filesystem

#580 2013-06-14 12:38:43

Re: filesystem Update Error /bin exists in filesystem

#581 2013-06-14 13:19:23

Re: filesystem Update Error /bin exists in filesystem

#582 2013-06-14 15:09:41

Re: filesystem Update Error /bin exists in filesystem

#583 2013-06-14 15:28:30

Re: filesystem Update Error /bin exists in filesystem

#584 2013-06-14 15:31:26

Re: filesystem Update Error /bin exists in filesystem

#585 2013-06-14 15:44:18

Re: filesystem Update Error /bin exists in filesystem

#586 2013-06-14 15:45:38

Re: filesystem Update Error /bin exists in filesystem

#587 2013-06-14 15:52:16

Re: filesystem Update Error /bin exists in filesystem

#588 2013-06-14 15:57:36

Re: filesystem Update Error /bin exists in filesystem

#589 2013-06-14 16:07:46

Re: filesystem Update Error /bin exists in filesystem

#590 2013-06-14 16:08:54

Re: filesystem Update Error /bin exists in filesystem

#591 2013-06-14 16:11:36

Re: filesystem Update Error /bin exists in filesystem

#592 2013-06-14 16:27:03

Re: filesystem Update Error /bin exists in filesystem

#593 2013-06-14 18:40:58

Re: filesystem Update Error /bin exists in filesystem

#594 2013-06-15 05:56:25

Re: filesystem Update Error /bin exists in filesystem

#595 2013-06-15 09:11:53

Re: filesystem Update Error /bin exists in filesystem

#596 2013-06-15 12:02:09

Re: filesystem Update Error /bin exists in filesystem

#597 2013-06-15 13:05:35

Re: filesystem Update Error /bin exists in filesystem

#598 2013-06-15 14:36:01

Re: filesystem Update Error /bin exists in filesystem

#599 2013-06-15 15:07:51

Re: filesystem Update Error /bin exists in filesystem

#600 2013-06-15 15:16:09

Re: filesystem Update Error /bin exists in filesystem

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